8WPS image
Entry Detail
PDB ID:
8WPS
Keywords:
Title:
Anabaena McyI R166M with prebound NAD and malate
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2023-10-10
Release Date:
2024-10-16
Method Details:
Experimental Method:
Resolution:
1.90 Å
R-Value Free:
0.20
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 31 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:McyI
Mutations:R166M
Chain IDs:A
Chain Length:357
Number of Molecules:1
Biological Source:Anabaena sp. 90
Primary Citation
Structural insights into the catalytic mechanism of the microcystin tailoring enzyme McyI.
Commun Biol 8 578 578 (2025)
PMID: 40195441 DOI: 10.1038/s42003-025-08008-9

Abstact

The most common cyanotoxin microcystin is a cyclic heptapeptide produced by non-ribosomal peptide-polyketide synthetases and tailoring enzymes. The tailoring enzyme McyI, a 2-hydroxyacid dehydrogenase, converts (3-methyl)malate into (3-methyl)oxaloacetate to produce the non-proteinogenic amino acid (3-methyl)aspartate. The reaction is NAD(P)-dependent but the catalytic mechanism remains unclear. Here we describe the crystal structures of McyI at three states: bound with copurified NAD, cocrystallized with NAD/NADP, and cocrystallized with malate or the substrate analogue citrate. An McyI protomer has unusual three nicotinamide cofactor-binding sites, named the NAD-prebound, NADP specific, and non-specific sites. Biochemical studies confirmed the NADP preference during oxidoreductase reaction. Molecular basis for McyI catalysis was revealed by the structures of McyI-NAD binary complex, McyI-NAD-NADP and McyI-NAD-malate ternary complexes, which demonstrate different opening angles between the substrate-binding domain and the nucleotide-binding domain. These findings indicate that McyI is a unique member of the 2-hydroxyacid dehydrogenase superfamily and provide detailed structural insights into its catalytic mechanism. In addition, the structural ensemble representing various binding states offers clues for designing enzyme for bioengineering applications.

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